In article <63nvhs$ghg at net.bio.net>, Brian Foley <btf at t10.lanl.gov> wrote:
> Andrew Mitchell wrote:
> > How does the outgroup polarize the character states?
> > Quite simply, the node joining the outgroup to the ingroup
> > is the most basal node in your phylogeny. If you insist
> > on looking at it on a character-by-character basis, then
> > that state found in the outgroup (assuming there is only
> > one outgroup taxon) is assumed to the primitive, thus
> > polarizing your states).
> Which phylogenetic methods do this (treat the outgroup
> as ancestral)? Are you saying that the outgroup "should be"
> treated as primitive? Or that is "is" treated as primitive by
> a ceertain method?
Andrew has correctly described the way that outgroup analysis was
originally intended to work. However, it is rarely applied in this way by
the commonly used computer programs, such as PAUP.
> If we have that following sequences:
>> 1 10 18
> outgroup: gaa cat tac ggc ggg cca
> species1: gaa caa atc ggc gga cct
> species2: gat caa atc gac gga cct
> species3: gat cag ttc gga ggg cgt
> I would suspect that at position 3 the ancestor was "a"
> as some of the ingroup as well as the outgroup have "a"
> here. However, at position 18, it is equally likely
> that the ancestor was "t" and the outgroup mutated to
> "a"; or the ancestor was "a" and the ingroup mutated
> to "t" before divergence of the 3 ingroup species.
Careful -- by using the "common = primitive" rule you are likely to
conflate synapomorphy with plesiomorphy on occasion. Specifically, you
are biasing your analysis in a way that will cause you to miss
synapomorphies deep in your ingroup. Those synapomorphies will be common,
but derived (not primitive).
> When PAUP generates an "ancestral" sequence, it does
> not just give you the outgroup sequence. I believe
> (but I'm not 100% sure) that you can generate such
> an ancestral sequence in PAUP using either a maximum
> likelyhood, or a maximum parsimony method.
Whether you use MP or ML in PAUP, it will estimate ancestral character
states that are different from the outgroup states because it does not use
the outgroup to polarize ingroup character states as Andrew described. It
builds an unrooted tree that includes the outgroup as a member of the
ingroup, then pulls down the node connecting the outgroup to the rest of
the network. It can be argued that this is a good way to use an outgroup,
but it is not outgroup rooting as originally described.
> I do not know of any program which allows us to add
> truly ancestral sequences (perhaps obtained from fossil
> DNA; or in the case of a rapidly evolving species such
> as HIV, from frozen blood samples) with dates, in order
> to more accurately determine the ancestral states.
Actually, I believe that PAUP* will allow you to insert ancestral
character states directly into the analysis; thus, polarizing characters
prior to building an ingroup tree as originally envisioned for outgroup
analysis.
--
Guy Hoelzer e-mail: hoelzer at med.unr.edu
Department of Biology phone: 702-784-4860
University of Nevada Reno fax: 702-784-1302
Reno, NV 89557